PDB-7aa9: Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1

ID or keywords:

Entry

Database: PDB / ID: 7aa9

Title

Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1

Components

Gamma-aminobutyric acid receptor-associated protein-like 1
pT13/PT15 SCOC LIR

Keywords

SIGNALING PROTEIN / SCOC / ATG8 / LIR

Function / homology

Function and homology information

glycophagy / Tat protein binding / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.72 Å

Authors

Lee, R. / Mouilleron, S. / Wirth, M. / Zhang, W. / O Reilly, N. / Dhira, J. / Tooze, S.

Citation

Journal: J.Mol.Biol. / Year: 2021
Title: Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity.
Authors: Wirth, M. / Mouilleron, S. / Zhang, W. / Sjottem, E. / Princely Abudu, Y. / Jain, A. / Lauritz Olsvik, H. / Bruun, J.A. / Razi, M. / Jefferies, H.B.J. / Lee, R. / Joshi, D. / O'Reilly, N. / ...

History

Deposition	Sep 3, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 16, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2023	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7aa9.cif.gz	440.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7aa9.ent.gz	301.3 KB	Display	PDB format
PDBx/mmJSON format	7aa9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7aa9_validation.pdf.gz	509.2 KB	Display	wwPDB validaton report
Full document	7aa9_full_validation.pdf.gz	514.9 KB	Display
Data in XML	7aa9_validation.xml.gz	38.6 KB	Display
Data in CIF	7aa9_validation.cif.gz	54.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aa/7aa9 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/7aa9	HTTPS FTP

-
Related structure data

Related structure data	7aa7C 7aa8C 6hoiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7aa7-1 7lk3-1 6i78-d 4c7a-1 7aa9-2 7ct3-d 4co7-1 4e6i-2 4j8t-1 6cqc-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7aa7C

7aa8C

6hoiS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (2)

Deposited unit

A: Gamma-aminobutyric acid receptor-associated protein-like 1

B: pT13/PT15 SCOC LIR

C: Gamma-aminobutyric acid receptor-associated protein-like 1

D: pT13/PT15 SCOC LIR

E: Gamma-aminobutyric acid receptor-associated protein-like 1

F: pT13/PT15 SCOC LIR

G: Gamma-aminobutyric acid receptor-associated protein-like 1

H: pT13/PT15 SCOC LIR

I: Gamma-aminobutyric acid receptor-associated protein-like 1

J: pT13/PT15 SCOC LIR

K: Gamma-aminobutyric acid receptor-associated protein-like 1

L: pT13/PT15 SCOC LIR

96.4 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gamma-aminobutyric acid receptor-associated protein-like 1

B: pT13/PT15 SCOC LIR

defined by author&software
Evidence: surface plasmon resonance
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Gamma-aminobutyric acid receptor-associated protein-like 1

D: pT13/PT15 SCOC LIR

defined by author&software
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Gamma-aminobutyric acid receptor-associated protein-like 1

F: pT13/PT15 SCOC LIR

defined by author&software
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Gamma-aminobutyric acid receptor-associated protein-like 1

H: pT13/PT15 SCOC LIR

defined by author&software
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Gamma-aminobutyric acid receptor-associated protein-like 1

J: pT13/PT15 SCOC LIR

defined by author&software
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Gamma-aminobutyric acid receptor-associated protein-like 1

L: pT13/PT15 SCOC LIR

defined by author&software
16.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.944, 90.944, 92.407
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂
Space group name Hall	P3₂
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3

#1: Protein	Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1 Mass: 14598.667 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide	pT13/PT15 SCOC LIR Mass: 1472.298 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1500 0.1M TRIS 8

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.72→59.94 Å / Num. obs: 90238 / % possible obs: 99.17 % / Redundancy: 3.9 % / B_iso Wilson estimate: 17.27 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.05 / Net I/σ(I): 7.55
Reflection shell	Resolution: 1.72→1.78 Å / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 8924 / CC_1/2: 0.57 / R_pim(I) all: 0.54

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.18.2_3874	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HOI

6hoi

Resolution: 1.72→59.94 Å / SU ML: 0.3086 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.3458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2614	4406	4.89 %
R_work	0.2096	85650	-
obs	0.212	90056	99.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→59.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6263	0	0	743	7006

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0016	6637
X-RAY DIFFRACTION	f_angle_d	0.4592	9068
X-RAY DIFFRACTION	f_chiral_restr	0.0438	944
X-RAY DIFFRACTION	f_plane_restr	0.0038	1177
X-RAY DIFFRACTION	f_dihedral_angle_d	21.9767	2504

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.72-1.74	0.3701	124	0.3699	2797	X-RAY DIFFRACTION	97.04
1.74-1.76	0.4048	161	0.3641	2780	X-RAY DIFFRACTION	96.81
1.76-1.78	0.399	152	0.3567	2811	X-RAY DIFFRACTION	97.08
1.78-1.8	0.4022	178	0.3474	2741	X-RAY DIFFRACTION	97.14
1.8-1.83	0.3827	170	0.3161	2778	X-RAY DIFFRACTION	96.53
1.83-1.85	0.3715	167	0.3197	2728	X-RAY DIFFRACTION	94.45
1.85-1.88	0.3626	152	0.2978	2777	X-RAY DIFFRACTION	99.19
1.88-1.91	0.3028	118	0.2988	2951	X-RAY DIFFRACTION	99.68
1.91-1.94	0.3514	158	0.2812	2834	X-RAY DIFFRACTION	99.6
1.94-1.97	0.3526	114	0.2571	2921	X-RAY DIFFRACTION	99.84
1.97-2	0.3116	192	0.2553	2788	X-RAY DIFFRACTION	99.8
2-2.04	0.2529	132	0.2501	2884	X-RAY DIFFRACTION	99.77
2.04-2.08	0.2972	138	0.2487	2911	X-RAY DIFFRACTION	99.93
2.08-2.12	0.3185	172	0.2472	2868	X-RAY DIFFRACTION	99.93
2.12-2.17	0.2875	192	0.228	2850	X-RAY DIFFRACTION	99.87
2.17-2.22	0.27	148	0.2176	2853	X-RAY DIFFRACTION	99.97
2.22-2.27	0.271	160	0.2075	2864	X-RAY DIFFRACTION	99.97
2.27-2.33	0.2513	178	0.2083	2856	X-RAY DIFFRACTION	100
2.33-2.4	0.2605	128	0.2083	2900	X-RAY DIFFRACTION	100
2.4-2.48	0.2439	144	0.2124	2856	X-RAY DIFFRACTION	99.97
2.48-2.57	0.2547	176	0.2069	2841	X-RAY DIFFRACTION	100
2.57-2.67	0.2673	122	0.2024	2919	X-RAY DIFFRACTION	100
2.67-2.79	0.2425	126	0.2001	2878	X-RAY DIFFRACTION	99.93
2.79-2.94	0.2714	98	0.2009	2969	X-RAY DIFFRACTION	99.97
2.94-3.13	0.2536	151	0.1877	2850	X-RAY DIFFRACTION	99.87
3.13-3.37	0.25	150	0.1706	2875	X-RAY DIFFRACTION	100
3.37-3.7	0.1963	140	0.1648	2892	X-RAY DIFFRACTION	100
3.71-4.24	0.1973	111	0.1469	2891	X-RAY DIFFRACTION	99.8
4.24-5.34	0.1711	134	0.1473	2895	X-RAY DIFFRACTION	99.7
5.34-59.94	0.1954	120	0.1852	2892	X-RAY DIFFRACTION	99.47

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.93988968936	-2.44009010722	0.662487214469	3.2284321078	1.71079324725	5.07090676609	-0.0903849133872	-0.684749947178	0.207879045863	0.554937028361	0.176442579334	0.218790993548	0.280282773618	0.106007248342	-0.0155361395277	0.218228348604	0.0721722607174	-0.0174522353862	0.345458252742	-0.0555164155632	0.157440416483	-18.7922860192	69.5902822389	3.50376371859
2	4.18070287634	0.174858129104	-4.31254475692	0.0159207995471	-0.230390559683	4.69873053023	0.206222233571	0.347982268467	0.687905816727	-0.0673240159162	-0.0109924653839	-0.0241441864652	-0.228348922264	-0.104796750582	-0.0219099326715	0.108275781526	0.0297419425114	-0.00558469351	0.14587548574	0.0404153928698	0.274986354066	-20.9266010072	73.6858734306	-9.05751940308
3	1.25008665792	-0.43075023313	0.54365854683	1.76521124327	-0.69849719452	2.50028801727	-0.0886276799408	-0.122804155098	0.0688911680429	0.159119721395	0.0811278513985	0.00485547021184	-0.399656716163	0.104686918357	-0.000461665739032	0.131687152987	-0.00254455045588	0.00370626461652	0.109630133419	0.00135183376608	0.118220175159	-8.22170221357	66.8050948849	-3.74468491451
4	2.71549247084	1.10173261027	2.15896653441	1.49461033986	2.13448950193	6.18345058459	-0.0979991729191	-0.17806979456	-0.0872880176471	0.265372194434	-0.058106307386	0.0407022598243	0.183164141466	0.333924644357	0.102732460786	0.122900573264	0.0326806895498	0.023867022364	0.145690958505	0.0125356017241	0.0955772725449	0.0315218774605	62.2261401965	-3.83205874193
5	0.956086141389	-0.492302383461	0.434289309216	1.73006980798	-0.138805526815	2.22002478657	-0.0374011178023	-0.0208018927225	0.0892595958436	0.165227454157	-0.00313861015811	-0.198663376898	0.000710481003825	0.0785975354043	0.0496637378801	0.142702001331	0.0196101681171	-0.0018655648641	0.117628281994	0.00753689747682	0.174088971114	-3.96085317289	56.6428741548	-0.232787645001
6	5.37534144319	-0.909803790312	-2.22529756644	5.26383582101	1.99080724856	4.29375053203	-0.00145698925562	0.277641956127	-0.155628888623	-0.131155155897	-0.130462475075	0.171814224337	0.151834280064	-0.274335150026	0.108755832374	0.104728335362	0.000650946988066	0.00239746392921	0.116151493054	0.0105299909015	0.106213029836	-17.5785478281	62.0907949676	-10.2742794162
7	1.79048813007	-1.69822200963	1.83270165266	2.05075501884	-1.80010417456	1.88003970656	-0.0176063145422	-0.274070353406	-0.154637428793	0.309568797536	0.101749914219	0.184363578031	-0.0714705470579	-0.13112811469	-0.178233394664	0.169736938671	0.0419753552413	0.0249362737514	0.15115013997	0.0385663643953	0.126669337234	-10.2528263932	57.6901788731	4.30698417166
8	7.58980172714	-4.98747027745	-1.94553657325	6.56083603288	2.11904437749	2.53138912869	-0.0146376437522	-0.519020752193	0.766388096566	-0.0050547213986	0.226737207956	-0.234648917595	-0.398184092648	0.269490442087	-0.120428017715	0.236377294935	-0.0497352398236	-0.0194288047713	0.162263972072	-0.0387347803582	0.24753027611	-4.35062339912	72.8636673298	-8.10295713532
9	0.587815253881	1.39500632383	-1.04406279677	4.58742138357	-1.77542076085	2.9681997858	0.0253903776285	-0.142013155414	-0.248772015199	0.268315203633	-0.105237192512	-0.34371102248	-0.195432062784	0.251164819876	0.0824073398762	0.449619396798	-0.0119997644712	0.0259885463198	0.0811177425643	0.0646697199743	0.147318710823	-3.14213891232	80.5372479122	-21.7811552143
10	2.22221092359	-1.61630100292	2.39682129129	4.21736064053	-3.54180451364	6.68357593326	-0.0869346555285	0.127808159323	-0.275524849342	-0.523965862172	0.0756651574001	0.407703082937	0.0207757944757	-0.171671203144	0.153309683506	0.305713611074	0.00679586661286	-0.057514729546	0.156010939302	-0.0288512722985	0.231994754704	-7.14150982419	76.2045014125	-34.4643417477
11	1.5197617487	0.0242027107339	-0.101444300319	2.01210362654	1.85850769151	4.03583551283	-0.0462174163191	-0.220162442906	-0.155706406063	0.0587185965859	-0.172702913707	0.196597552931	-0.00936099985097	-0.588590754624	0.139781302416	0.247840379775	-0.0250939566429	-0.0359272686205	0.177088759865	0.0129167322753	0.131531580105	-7.58964561717	90.1230401114	-25.4268138169
12	1.93718198084	-0.19247860638	-0.518563710257	2.09436631842	0.0694278697224	2.42105266205	0.0435489130261	-0.211535885294	-0.112529779551	0.13304101845	-0.0526578403669	0.0473059188158	0.0406347008621	0.044062224126	0.00974565070396	0.14485531531	-0.00503851757577	-0.0169151377863	0.150280484433	0.0286013876961	0.10879130777	-7.88076890967	96.9213275638	-31.9276273242
13	1.15280895567	0.625585104296	-0.200069174048	2.02707303098	0.489117479197	2.8272690924	0.166660312915	-0.156428321086	0.164214382373	-0.0160425773143	-0.207345602573	0.0703396669793	-0.14657453781	-0.0998689406895	0.0713216014715	0.127573315413	-0.0194987473299	-0.0164442892189	0.130668154938	-0.0250080280931	0.140680618195	-0.748776307279	99.6550667923	-25.7845013902
14	3.42988397232	-0.291367368977	0.137799479061	5.98729264582	-0.913505843477	1.84695418258	-0.00305655019562	0.175540047735	-0.0821070217009	-0.352693609245	-0.057062677867	-0.386931092532	0.22830036134	0.172623646457	0.0597738613069	0.195106715072	0.0262763014113	0.00607475354654	0.114769682745	-0.00793862316436	0.111542430909	0.828959286298	85.0331344728	-35.6500471712
15	0.602806013119	0.684005447673	0.397528029161	2.41399022014	1.99770912145	1.81943876264	0.0834867726365	-0.0285849379634	0.0240390796927	0.333240952716	0.0381084667711	-0.177688056256	0.184580220753	0.31157843817	-0.137571292939	0.208630372124	-0.00124237730711	-0.052052624396	0.145138271059	0.0139243247126	0.130824989558	1.1559994487	93.7029479904	-21.1750853041
16	0.943236651693	2.2164146582	-1.37024145655	6.27491753621	-3.60282460198	2.33550603362	0.19567381391	-0.263846184976	-0.199256584376	0.266769622228	0.173693259714	0.750647182813	0.166550530817	-0.466385468329	-0.304599243667	0.285571449736	-0.0649550132542	-0.0272557891116	0.276352038219	0.114540863837	0.357873756516	-15.4678216509	90.5934727765	-33.1866683755
17	6.54301226878	3.58760848245	1.00054703941	4.48761668675	-0.0735574538224	3.20109793711	-0.144263453001	0.819401090348	0.0506674772214	-0.487860653113	0.403351643389	-0.243775220819	-0.0565731758319	-0.107764327182	-0.190805643763	0.117333389593	-0.016617432208	0.0031106700385	0.377102631609	-0.00135250961345	0.140912315226	21.1161077177	66.8804724404	-33.5705811311
18	0.976346275618	0.327491191589	0.237096500085	0.786736272969	0.110310717532	0.651825806229	0.0202670253155	-0.419346170571	0.418159689904	0.103776414515	-0.123029860584	-0.132981591406	-0.0799813463067	-0.0436868106473	-0.18361057392	0.0212680084698	-0.181174327777	-0.00800278690845	0.411375170994	-0.0876247628778	0.288908362542	23.4001857716	70.7759260235	-20.7703953966
19	2.25600246357	0.684456527797	1.57011618983	1.53756362575	0.141163027464	2.78531360267	-0.109073367091	-0.0697107728464	0.306348489915	-0.105839839541	-0.157286399556	0.0624219844262	-0.356706720286	-0.0759906570277	0.246536476945	0.124532206867	-0.0177404861523	0.0139647634464	0.191161980395	-0.0425837209444	0.137606726683	10.2291585776	65.8308705763	-29.871132098
20	1.58538012399	0.189403109668	-0.559872889197	1.43524167354	-0.0962832053386	1.4330105086	-0.0116416224604	-0.135109942279	-0.0527976501095	0.01723041518	-0.0418072910887	-0.0193124126819	-0.0409859850365	0.0823133494948	0.0335745523501	0.0937050877811	-0.0138350686317	0.00759852257645	0.139648290051	-0.00315090973743	0.110615184461	8.75571577626	59.4276525726	-25.3251613428
21	0.986065335097	0.717340015905	-1.32279478427	2.37212579357	-1.55765859219	2.07273281706	-0.0501204475191	0.22086740054	-0.27153960271	-0.169055308322	-0.236850773422	-0.864634017909	0.0631159173706	0.91634844733	0.130966516968	0.205620213721	-0.00335235971582	0.0348611620718	0.283476667127	-0.0188570693882	0.277132450167	9.376141325	52.1319600234	-38.4648074452
22	7.60488563698	3.09783850978	-2.83480123953	3.11167529401	-1.47055893203	2.46506421931	-0.168186273043	0.229022297065	0.717213107527	-0.189822264079	0.197546115469	-0.0439884957835	-0.229063997569	-0.0660542509249	-0.0807068909273	0.216108083	-0.0112508106146	0.0278676978533	0.187999814878	0.0333917739942	0.250518709057	6.14988400345	72.3211685248	-22.19688355
23	0.604582919763	0.270564558424	-1.28932956227	7.02236219264	0.498295457084	2.91139044098	0.0283706044725	0.480798672337	-0.692636708996	-0.355229088234	0.222481988303	-0.0297170811989	0.252235976215	0.0459098535843	-0.150305957447	0.280131311369	-0.0149160593081	-0.0271736208808	0.261718484534	-0.129209692672	0.355607762277	2.88178876487	79.5744916979	2.4522672358
24	1.83291447871	2.17990831629	2.92498777891	3.30846755889	3.51832709817	5.39961521811	0.0631992047589	-0.0133254024973	-0.756534030053	0.0735166610622	0.177495721896	-0.307879683958	0.301918458136	0.0369046831092	-0.0412938404485	0.187728785075	-0.00591673334086	-0.0316048116684	0.133744092914	-0.0119378887721	0.515739689728	5.50758676531	75.594256462	15.665328912
25	1.92096895355	-0.399354668467	0.313818344882	1.88110897111	-0.298110253507	1.04801312295	0.0464541307134	-0.0150088624881	-0.16107463562	-0.0132648805691	0.0811049475032	-0.110650195573	0.133832642327	0.0414495355519	-0.0419853186711	0.0818959817798	0.0297407554487	-0.0443989763274	0.11544894465	-0.0229022663324	0.171633638371	6.82920533751	86.8157833159	14.427313771
26	0.716211578476	-0.14921362589	0.639561354672	0.870056648303	-1.04579641517	3.09004127678	0.0514721019425	0.159585739522	-0.139206018911	-0.183240742962	-0.0132219415278	-0.00610642641802	0.176715522713	0.193356627651	-0.0260548549474	0.14997104687	-0.00116204753228	-0.0294688022187	0.169839808973	-0.0191592909563	0.167453799693	7.27499684935	91.6964736513	6.88008619751
27	3.57020388974	0.203585388122	-2.13135297854	1.44836316273	-0.00428492043474	4.15747429524	0.00904273509814	0.231137317095	-0.129238741936	-0.255528199998	-0.21943905968	-0.0430800348762	-0.377987830813	0.0513418065848	0.126600947041	0.136282623045	0.00438022893175	-0.0405277316214	0.156203247583	-0.0227019973388	0.100720761373	7.43440437586	99.3148625706	9.64059075627
28	0.915726388971	-0.405576989342	-0.207518462982	1.81485117754	-0.303792631123	2.92110184975	0.076989554207	0.116520767453	-0.0383552886614	-0.0545001997251	-0.0338574390335	-0.138444367581	-0.0558890452767	-0.105385741351	-0.0307230153289	0.10779794371	0.0186435744958	-0.0359277767036	0.150878025638	-0.0214072457651	0.189573204562	0.177047417671	98.8564918752	6.72063942151
29	7.8594231491	-1.07981734329	0.744495839666	8.41479931625	0.629381534133	1.37855277887	-0.15910251659	-0.0832420036993	-0.150125813951	-0.0250996541798	0.0109127166117	0.35075403161	0.168077451287	-0.448188788004	0.0971879223929	0.105394531518	-0.0113018161229	-0.0480449839402	0.176032578577	0.0190563255936	0.156274672423	-2.99588322494	89.0988065758	18.2243007677
30	8.82110893967	1.77665801021	-0.863388186461	4.25960591799	2.39349595035	2.04827148089	-0.0802111671448	-0.0160584592828	-0.728313994035	0.160535604377	-0.0340833098818	0.265847005865	0.466255488055	0.0195955960337	0.090352351839	0.191416474836	-0.0717711707618	-0.0412559867913	0.166308688479	0.00615760767711	0.290808119629	-0.935900569854	79.8833387415	14.1785211359
31	0.724753462033	-0.390410678752	-0.385022596501	3.23029898113	-1.68667722159	1.63111912887	0.125922527402	0.31423365511	-0.259248891382	-0.385470039114	0.0531031897722	0.293554642876	0.104553350732	-0.0735693640279	-0.221281400175	0.168086566254	0.000132036560457	-0.0533555165368	0.211275449846	-0.0358842870634	0.165533688092	-1.65737729551	93.4768907208	1.61871769392
32	2.15043406722	0.205484145595	0.233984548573	1.66424724338	1.88205743923	4.70282250532	-0.0242611229959	0.365508686486	-0.266016064275	-0.253102645644	0.213955040121	-0.717134383533	0.0976254405619	0.709411533705	-0.15978314373	0.134926789247	-0.00765060994917	0.00820806288172	0.269350925907	-0.0673072502832	0.291771983364	14.7090521853	89.1767016056	13.4974855808
33	6.37730680217	3.74816982091	0.317142431021	5.74256172579	-1.60582253872	4.81940692088	-0.0801562371475	0.180255259749	-0.226661966774	-0.464889452261	0.163525216482	-0.334560891477	0.258896020464	0.0302411116645	-0.0512947742504	0.15382657094	-0.0275674218098	0.02126105773	0.206661474758	-0.000992290872891	0.128213504642	-25.9953512933	95.5931339492	-34.7702412345
34	1.72314364953	0.90545769799	0.310381846221	1.70899548243	0.221504575778	1.02793563172	0.157177638209	-0.347348458185	0.126191234414	0.159409708223	-0.0937156678703	-0.0924471913036	-0.0996490729361	0.212743430885	-0.0222554358748	0.123948524195	-0.0690692831292	0.0199174602	0.189677131269	-0.0430455828205	0.145624790904	-29.4677848842	97.6658190541	-22.7260329063
35	0.83406045773	-0.0371360669591	0.545112602347	0.658472942793	-0.00100331527621	2.05735296667	0.00364673984956	0.0877119126205	0.0753301672844	-0.051233220897	-0.039035506605	-0.0165917443026	0.0543933321817	0.129558351462	0.0334164238788	0.118290746904	-0.013507480999	0.0228686378995	0.118388075895	-0.00559413859519	0.0982637243985	-41.3196254884	90.2203910882	-30.3844726152
36	0.801786450929	-0.169577135728	0.52085122807	2.01587041094	-0.440910713658	2.34195671253	-0.00562457294133	-0.0428937490044	-0.0559641335388	-0.257130593817	0.0407612251047	0.00865468982447	0.0660527560534	-0.081038928509	-0.0522855266496	0.122145288109	-0.0365282504986	0.0110329197853	0.107088345198	-0.0264399661437	0.136171074896	-40.9224663292	82.1642924337	-31.7013193723
37	4.19711974653	-0.237887889606	-0.996045040343	2.94811118912	-0.384751932656	1.61414323668	-0.0839977651572	-0.397094951818	-0.116687216536	0.250384158099	-0.131678972035	-0.309834364826	0.0665567415487	0.426426699516	0.0986559526547	0.0888784265144	-0.0283129291521	-0.0334103341342	0.18671167326	0.0021843705008	0.117567943355	-28.521781087	88.4878908644	-21.3146849143
38	3.40524919411	2.88864523767	3.01849979923	3.39191680412	2.1002711318	2.92509492405	-0.0400509799639	0.472017107188	-0.450690989237	-0.376972917694	0.297244117266	-0.558548143071	0.169816593227	0.483454001992	-0.251427189804	0.155066148973	-0.0271193905826	0.0507817541565	0.141976871798	-0.0366254311713	0.168538898397	-34.9638361356	83.9467561907	-35.5248811498
39	6.99126420692	0.825532817728	-3.03583071242	4.44135431182	-2.89186511096	6.9548685622	0.148221712044	-0.0434301802369	0.357163375466	0.150582571713	-0.0871733899566	0.172209258676	-0.590800737006	0.139991404405	-0.154237248944	0.174558532345	-0.0132813559081	0.00441499593537	0.143600096407	0.0119617954896	0.132080896519	-40.9476175523	99.5226428212	-24.5593058181
40	2.42790010897	-0.671301929377	0.692986997037	1.29420171427	0.142284584526	1.29567367878	0.083654385185	-0.124011240605	0.240624023902	0.167454645466	-0.00360321339931	0.431375328823	-0.251841438326	-0.123594489908	-0.0741780980515	0.21785621177	0.051617370525	0.0775948507823	0.147016445907	0.00371466637509	0.284025086483	26.0074308251	95.2562488992	-8.02174368654
41	1.24825907837	-0.000160790295792	0.551724355879	1.28882483335	-0.385110715541	1.66892880735	-0.0135610309129	-0.048672803611	0.0362672088937	0.147438233601	-0.0426379638256	0.137286550363	0.0426949064724	-0.047385107392	0.046315961442	0.141683471641	0.00882793530547	0.0379413716158	0.0744215972035	-0.00662904521425	0.116353791511	36.5212172148	86.1446337982	-4.12386917582
42	3.28785684351	-1.84732262469	-1.47383581013	5.01794410903	2.08208866193	2.95419420467	-0.0300913261356	-0.123132198112	0.584195126144	-0.199297001708	0.263527452499	-0.0169737429773	-0.728796870342	0.404011428375	-0.177275247024	0.263600904477	-0.0353800559696	0.0571561525456	0.235794048145	-0.00106795540273	0.202705874043	39.0012990544	98.9619748638	-10.0157299782

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 10 )	A	A	1 - 10	1 - 10
2	2	chain 'A' and (resid 11 through 24 )	A	A	11 - 24	11 - 24
3	3	chain 'A' and (resid 25 through 56 )	A	A	25 - 56	25 - 60
4	4	chain 'A' and (resid 57 through 68 )	A	A	57 - 68	61 - 72
5	5	chain 'A' and (resid 69 through 90 )	A	A	69 - 90	73 - 100
6	6	chain 'A' and (resid 91 through 104 )	A	A	91 - 104	101 - 116
7	7	chain 'A' and (resid 105 through 117 )	A	A	105 - 117	117 - 129
8	8	chain 'B' and (resid 12 through 20 )	B	B	12 - 20	1 - 9
9	9	chain 'C' and (resid 0 through 10 )	C	C	0 - 10	1 - 11
10	10	chain 'C' and (resid 11 through 24 )	C	C	11 - 24	12 - 27
11	11	chain 'C' and (resid 25 through 47 )	C	C	25 - 47	28 - 50
12	12	chain 'C' and (resid 48 through 68 )	C	C	48 - 68	51 - 75
13	13	chain 'C' and (resid 69 through 90 )	C	C	69 - 90	76 - 101
14	14	chain 'C' and (resid 91 through 104 )	C	C	91 - 104	102 - 115
15	15	chain 'C' and (resid 105 through 117 )	C	C	105 - 117	116 - 128
16	16	chain 'D' and (resid 12 through 21 )	D	D	12 - 21	1 - 10
17	17	chain 'E' and (resid 1 through 10 )	E	E	1 - 10	1 - 10
18	18	chain 'E' and (resid 11 through 24 )	E	E	11 - 24	11 - 24
19	19	chain 'E' and (resid 25 through 47 )	E	E	25 - 47	25 - 47
20	20	chain 'E' and (resid 48 through 110 )	E	E	48 - 110	48 - 120
21	21	chain 'E' and (resid 111 through 117 )	E	E	111 - 117	121 - 127
22	22	chain 'F' and (resid 12 through 21 )	F	F	12 - 21	1 - 11
23	23	chain 'G' and (resid 1 through 10 )	G	G	1 - 10	1 - 10
24	24	chain 'G' and (resid 11 through 24 )	G	G	11 - 24	11 - 24
25	25	chain 'G' and (resid 25 through 35 )	G	G	25 - 35	25 - 35
26	26	chain 'G' and (resid 36 through 56 )	G	G	36 - 56	36 - 58
27	27	chain 'G' and (resid 57 through 68 )	G	G	57 - 68	59 - 72
28	28	chain 'G' and (resid 69 through 90 )	G	G	69 - 90	73 - 98
29	29	chain 'G' and (resid 91 through 98 )	G	G	91 - 98	99 - 106
30	30	chain 'G' and (resid 99 through 104 )	G	G	99 - 104	107 - 112
31	31	chain 'G' and (resid 105 through 117 )	G	G	105 - 117	113 - 125
32	32	chain 'H' and (resid 12 through 20 )	H	H	12 - 20	1 - 9
33	33	chain 'I' and (resid 1 through 10 )	I	I	1 - 10	1 - 10
34	34	chain 'I' and (resid 11 through 35 )	I	I	11 - 35	11 - 35
35	35	chain 'I' and (resid 36 through 67 )	I	I	36 - 67	36 - 71
36	36	chain 'I' and (resid 68 through 90 )	I	I	68 - 90	72 - 96
37	37	chain 'I' and (resid 91 through 104 )	I	I	91 - 104	97 - 110
38	38	chain 'I' and (resid 105 through 115 )	I	I	105 - 115	111 - 121
39	39	chain 'J' and (resid 12 through 20 )	J	J	12 - 20	1 - 9
40	40	chain 'K' and (resid 1 through 35 )	K	K	1 - 35	1 - 35
41	41	chain 'K' and (resid 36 through 117 )	K	K	36 - 117	36 - 127
42	42	chain 'L' and (resid 12 through 21 )	L	L	12 - 21	1 - 10

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi